[2024-01-24 13:31:44,234] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:44,236] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:44,236] [INFO] DQC Reference Directory: /var/lib/cwl/stg739e6414-d77c-4b4f-85b7-4b0e530cff2e/dqc_reference
[2024-01-24 13:31:45,468] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:45,469] [INFO] Task started: Prodigal
[2024-01-24 13:31:45,469] [INFO] Running command: gunzip -c /var/lib/cwl/stg3d4ab014-d8fb-4bec-9940-06ca2808590f/GCF_009901525.1_ASM990152v1_genomic.fna.gz | prodigal -d GCF_009901525.1_ASM990152v1_genomic.fna/cds.fna -a GCF_009901525.1_ASM990152v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:06,427] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:06,427] [INFO] Task started: HMMsearch
[2024-01-24 13:32:06,427] [INFO] Running command: hmmsearch --tblout GCF_009901525.1_ASM990152v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg739e6414-d77c-4b4f-85b7-4b0e530cff2e/dqc_reference/reference_markers.hmm GCF_009901525.1_ASM990152v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:06,761] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:06,762] [INFO] Found 6/6 markers.
[2024-01-24 13:32:06,810] [INFO] Query marker FASTA was written to GCF_009901525.1_ASM990152v1_genomic.fna/markers.fasta
[2024-01-24 13:32:06,811] [INFO] Task started: Blastn
[2024-01-24 13:32:06,811] [INFO] Running command: blastn -query GCF_009901525.1_ASM990152v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg739e6414-d77c-4b4f-85b7-4b0e530cff2e/dqc_reference/reference_markers.fasta -out GCF_009901525.1_ASM990152v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:07,550] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:07,558] [INFO] Selected 10 target genomes.
[2024-01-24 13:32:07,558] [INFO] Target genome list was writen to GCF_009901525.1_ASM990152v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:07,563] [INFO] Task started: fastANI
[2024-01-24 13:32:07,564] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d4ab014-d8fb-4bec-9940-06ca2808590f/GCF_009901525.1_ASM990152v1_genomic.fna.gz --refList GCF_009901525.1_ASM990152v1_genomic.fna/target_genomes.txt --output GCF_009901525.1_ASM990152v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:18,841] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:18,842] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg739e6414-d77c-4b4f-85b7-4b0e530cff2e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:18,842] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg739e6414-d77c-4b4f-85b7-4b0e530cff2e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:18,855] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:32:18,855] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:18,856] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Kordia antarctica	strain=IMCC3317	GCA_009901525.1	1218801	1218801	type	True	100.0	1831	1833	95	conclusive
Kordia aestuariivivens	strain=YSTF-M3	GCA_014397005.1	2759037	2759037	type	True	83.7446	1138	1833	95	below_threshold
Kordia algicida	strain=OT-1	GCA_000154725.1	221066	221066	type	True	81.4095	981	1833	95	below_threshold
Kordia jejudonensis	strain=SSK3-3	GCA_001005315.1	1348245	1348245	type	True	81.0534	947	1833	95	below_threshold
Kordia periserrulae	strain=DSM 25731	GCA_003054265.1	701523	701523	type	True	79.7297	800	1833	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	76.9144	126	1833	95	below_threshold
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	76.8312	137	1833	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	76.7367	193	1833	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	76.6609	141	1833	95	below_threshold
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	76.5273	88	1833	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:18,857] [INFO] DFAST Taxonomy check result was written to GCF_009901525.1_ASM990152v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:18,858] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:18,858] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:18,858] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg739e6414-d77c-4b4f-85b7-4b0e530cff2e/dqc_reference/checkm_data
[2024-01-24 13:32:18,860] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:18,919] [INFO] Task started: CheckM
[2024-01-24 13:32:18,920] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009901525.1_ASM990152v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009901525.1_ASM990152v1_genomic.fna/checkm_input GCF_009901525.1_ASM990152v1_genomic.fna/checkm_result
[2024-01-24 13:33:23,356] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:23,358] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:23,380] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:23,380] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:23,381] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009901525.1_ASM990152v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:23,381] [INFO] Task started: Blastn
[2024-01-24 13:33:23,381] [INFO] Running command: blastn -query GCF_009901525.1_ASM990152v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg739e6414-d77c-4b4f-85b7-4b0e530cff2e/dqc_reference/reference_markers_gtdb.fasta -out GCF_009901525.1_ASM990152v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:24,514] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:24,517] [INFO] Selected 6 target genomes.
[2024-01-24 13:33:24,517] [INFO] Target genome list was writen to GCF_009901525.1_ASM990152v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:24,524] [INFO] Task started: fastANI
[2024-01-24 13:33:24,524] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d4ab014-d8fb-4bec-9940-06ca2808590f/GCF_009901525.1_ASM990152v1_genomic.fna.gz --refList GCF_009901525.1_ASM990152v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009901525.1_ASM990152v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:35,034] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:35,044] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:35,045] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_009901525.1	s__Kordia antarctica	100.0	1831	1833	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Kordia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014397005.1	s__Kordia aestuariivivens	83.7365	1139	1833	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Kordia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000154725.1	s__Kordia algicida	81.4608	974	1833	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Kordia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001005315.1	s__Kordia jejudonensis	81.0684	945	1833	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Kordia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003352465.1	s__Kordia sp003352465	80.1787	880	1833	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Kordia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006383075.2	s__Kordia sp006383075	79.6553	782	1833	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Kordia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:35,047] [INFO] GTDB search result was written to GCF_009901525.1_ASM990152v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:35,048] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:35,052] [INFO] DFAST_QC result json was written to GCF_009901525.1_ASM990152v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:35,052] [INFO] DFAST_QC completed!
[2024-01-24 13:33:35,053] [INFO] Total running time: 0h1m51s